Global molecular structure and interfaces: Refining an RNA : RNA complex structure using solution X-ray scattering data

Determining the global architecture of multicomponent systems is a central problem in understanding biomacromolecular machines. Defining interfaces among components and the global structure of multicomponent systems is a central problem in understanding the biological interactions on a molecular level. We demonstrate that solution X-ray scattering data can be used to precisely determine intermolecular interfaces from just the subunit structures, in the complete absence of intermolecular NMR restraints using an example of a 30 kDa RNA-RNA complex. The backbone root-mean-square deviation (rmsd) between structures that are determined using the scattering data and using intermolecular distance restraints is about 0.4 angstrom. Further, we refined the global structure of the complex using scattering data as a global restraint. The rmsd in backbone structures that are determined with and without the scattering data refinement is about 3.2 angstrom, suggesting the impact of the refinement to the overall structure. Information about the "global correctness" of solution RNA structures could not be practically obtained otherwise, due to the molecular nature of the RNA molecules, but could only be defined by the scattering data together by residual dipolar couplings. This method provides a powerful new approach for refining global structures of macromolecular complexes whose subunits are elongated.

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